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Ascend, Cardinal, Pitzer
Sometimes the best way to get access to a piece of software on the HPC systems is to install it yourself as a "local install". This document will walk you through the OSC-recommended procedure for maintaining local installs in your home directory or project space. The majority of this document describes the process of "manually" building and installing your software.
Pitzer
BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
Availability and Restrictions
Versions
The following versions of BamTools are available on OSC clusters:
Ascend, Cardinal, Pitzer
STAR: Spliced Transcripts Alignment to a Reference.
Availability and Restrictions
Versions
The following versions of STAR are available on OSC clusters:
Ascend, Pitzer
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Availability and Restrictions
Versions
The following versions of Trimmomatic are available on OSC clusters:
Pitzer
bam2fastq is used to extract raw sequences (with qualities) from programs like SAMtools, Picard, and Bamtools.
Availability and Restrictions
Versions
The following versions of bam2fastq are available on OSC clusters:
Ascend, Cardinal
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).
Availability and Restrictions
Versions
The following versions of SnpEff are available on OSC clusters:
Cardinal, Pitzer
The Sequence Read Archive (SRA Toolkit) stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Use SRA Toolkit tools to directly operate on SRA runs.
Ascend, Cardinal, Pitzer
Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc.
Availability and Restrictions
Versions
The following versions of Ncview are available on OSC clusters:
Cardinal
The Subread package comprises a suite of software programs for processing next-gen sequencing read data like Subread, Subjunc, featureCounts, and exactSNP.
Availability and Restrictions
Versions
The following versions of Subread are available on OSC clusters:
Ascend, Cardinal, Pitzer
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
Availability and Restrictions
The following versions of VCFtools are available on OSC clusters:
